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Toxicoepigenetics : core principles and applications /
Toxicoepigenetics: Core Principles and Applications examines epigenetics, including chromatin biology, DNA methylation and non-coding RNA, along with fundamental techniques and considerations for studying each of these mechanisms of epigenetic regulation. Epigenetics have taken center stage in the s...
| Clasificación: | Libro Electrónico |
|---|---|
| Otros Autores: | , |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
London, United Kingdom :
Academic Press,
[2019]
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| Edición: | First edition. |
| Temas: | |
| Acceso en línea: | Texto completo |
Tabla de Contenidos:
- Front Cover
- Toxicoepigenetics: Core Principles and Applications
- Copyright
- Contents
- Contributors
- Editors' Biography
- Introduction to the Role of the Epigenome in Health and Disease
- Section 1: Histone Modifications and Chromatin Structure
- Chapter 1-1: Role of Histone Acetylation and Acetyltransferases in Gene Regulation
- Introduction
- History and Overview
- Nucleosome Assembly
- Chromatin Folding
- Gene Expression
- DNA Damage Repair
- Toxicoepigenetic Relevance
- Histone Acetyltransferases
- Families and Structures
- Regulation of HATs
- Transcriptional Activation
- HAT Complexes
- SAGA Transcription Regulatory Complex
- NuA4 Transcription Regulatory Complex
- Elongator Complex
- Chromatin Remodeling Complexes
- Global Histone Acetylation
- Role of Histone Acetyltransferases in Gene Activation
- Recruitment of Transcriptional Machinery
- Active Genes
- Inducible/Repressed Genes
- Environmental Exposure
- Histone Deacetylases
- Families
- Catalytic Mechanisms and Structures
- Regulation of HDAC Activity
- Role of HDACs at Active Genes
- Deacetylation and Gene Repression
- HDAC Complexes
- Conclusion and Perspectives
- References
- Chapter 1-2: The Role of Histone Methylation and Methyltransferases in Gene Regulation
- Introduction
- Site Specificity of Histone Methylation
- Lysine Methylation
- H2BK5 Methylation
- H3K4 Methylation
- H3K9 Methylation
- H3K27 Methylation
- H3K36 Methylation
- H3K79 Methylation
- H4K20 Methylation
- H4K5 Methylation
- Arginine Methylation
- Glutamine Methylation
- Regulation of Histone Methylation
- Posttranscriptional Modifications
- Noncoding RNAs
- Regulation of Xenobiotic Biotransformation-Related Genes by Histone Methylation
- Histone Methylation and Human Diseases
- Histone Methylation and Cancer.
- Histone Methylation and Neurological Disorders
- Histone Methylation and Other Diseases
- Histone Methylation and the Toxicity of Chemicals
- Heavy Metals
- Endocrine Disruptors (EDCs)
- Human Genotoxic Chemical Carcinogens From Occupational and Environmental Exposure
- Other Xenobiotics
- Conclusion
- References
- Chapter 1-3: Chromatin Accessibility as a Strategy to Detect Changes Associated With Development, Disease, and Exposure a ...
- Chromatin Accessibility as a Marker of Cell Lineage
- Methods for Determining Chromatin Architecture and Accessibility
- DNase I Hypersensitivity Assays
- Micrococcal Nuclease Assays
- Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE)
- Assay for Transposase-Accessible Chromatin (ATAC)
- Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
- Single Cell Assays for Determining Chromatin Accessibility in Heterogenous Cell Populations
- Chromatin Accessibility and Disease
- Understanding How Environmental Factors Influence Chromatin Accessibility
- Chromatin Accessibility and Cancer
- Chromatin Signature as a Diagnostic and Therapeutic Target in Cancer
- References
- Further Reading
- Chapter 1-4: Implications for Chromatin Biology in Toxicology
- Changes in Chromatin Modification States Are Important in Aging and the Developmental Origins of Health and Disease
- Mechanisms by Which Toxicant Exposures Alter the Chromatin Landscape
- Repressive Histone Marks and Polycomb Group Proteins
- Xenoestrogens
- Arsenic
- COMPASS Complex
- Xenoestrogens
- Arsenic
- The Histone Methyltransferase G9a
- Phthalates
- Arsenic
- Histone Acetylation
- Organotins
- Phthalates
- Dioxin
- Lead
- Chromium
- Arsenic
- Applications of Chromatin Biology to Toxicological Studies
- Summary
- References
- Section 2: DNA Methylation.
- Chapter 2-1: The Role of DNA Methylation in Gene Regulation
- Chapter Overview
- Introduction
- Mechanisms of DNA Methylation
- De Novo DNA Methylation
- Maintenance DNA Methylation
- DNA Methylation Patterns and the Developing Organism
- X-Chromosome Inactivation
- Imprinted Genes and Development
- Transposable Elements
- DNA Methylation as a Regulator of Gene Expression
- DNA Methylation in Gene Promoters Affects Transcription Factor Binding and Vice Versa
- DNA Methylation Recruits Methyl-CpG Binding Proteins and Remodels Chromatin
- DNA Methylation in the Gene Body Impacts Transcription
- DNA Demethylation
- TET-Mediated Oxidation and Demethylation
- Applications of DNA Methylation in Understanding and Treating Disease
- Environmental Links to DNA Methylation
- DNA Methylation as a Biomarker for Identifying and Understanding Disease
- DNA Methylation in Disease Therapy
- References
- Chapter 2-2: Implications of DNA Methylation in Toxicology
- Introduction
- Detection of DNA Methylation
- Bisulfite Methods of DNA Methylation Detection
- Direct Methods of Locus-Specific or Global DNA Methylation Detection
- Direct Methods of Genome-Wide DNA Methylation Detection
- Principles of DNA Methylation Modification
- Conservation of DNA Methylation Dynamics
- Diet-Induced Changes to DNA Methylation
- Evolutionary Conservation in Diet and DNA Methylation
- Background Diet Considerations in Rodents
- Caloric Restriction and DNA Methylation
- Macronutrient Restriction
- Macronutrient Shifts
- Micronutrient or Trace Mineral Deficiencies
- Pharmaceuticals
- Metals
- Metals as Toxicants
- High Density Metals
- Light Metals
- Organic Toxicants
- Nonchemical Stress
- Future Directions
- References
- Chapter 2-3: DNA Methylation as a Biomarker in Environmental Epidemiology.
- Methylomics as a Potential Biomarker for Both Disease and Toxic Exposures
- Methylomics of WBCs in Relation to Disease Causation and Toxic Exposures
- Methodological Considerations in Methylome-Wide Association Studies
- Platforms That Assess Single-Base Resolution Methylation
- Array-Based: MethylationEPIC BeadChip (Infinium) Microarray
- Next-Generation Sequencing
- Preprocessing and Normalization
- MethylationEPIC BeadChip (Infinium) Microarray
- Bisulfite Sequencing
- Addressing Confounding
- Inclusion of Technical Replicates
- Calculation for Differentially Methylated Sites
- Calculation for Differentially Methylated Regions
- Methylomics as a Potential Biomarker for Both Disease and Toxic Exposures
- Example: Smoking and AHRR Methylation
- Example: Air Pollution and DNA Methylation
- Example: Biological Aging as Measured by the Epigenetic Clock
- Example: VTRNA2-1 as a Metastable Epiallele
- Example: Epigenetic Pathway Linking Prenatal Maternal Stress and Wheeze in Children
- Conclusion
- References
- Chapter 2-4: DNA Hydroxymethylation: Implications for Toxicology and Epigenetic Epidemiology
- Introduction
- Chemistry of DNA Hydroxymethylation
- The Sixth-Base of Cytosine
- Distribution of 5-hmC in the Genome
- Changes in 5-hmC Level During Development
- Measurement of 5-hmC
- Global 5-hmC Measurement
- Locus-Specific 5-hmC Measurement
- DNA Immunoprecipitation (DIP)
- Enzymatic and Chemical Modifications
- Single Molecule Detection
- Exposures to Environmental Toxicants/Stressors and Changes in 5-hmC
- Heavy Metals
- Environmental Estrogens
- Air Pollutants
- Pesticides
- Ionizing Radiation
- Lifestyle
- Aging
- Discussion and Future Directions
- Acknowledgments
- References
- Section 3: Noncoding RNAs
- Chapter 3-1: The Role of Noncoding RNAs in Gene Regulation
- Introduction.
- Overview of Noncoding RNAs
- Transfer and Ribosomal RNA
- Long Noncoding RNA (lncRNA)
- Competitive Endogenous RNA
- Long Intervening Noncoding RNA
- Enhancer RNA
- Short Noncoding RNA
- Piwi-Interacting RNA
- Small Nuclear RNA
- Short Nucleolar RNA
- MicroRNA
- Short Interfering RNA
- MicroRNA Discovery
- MicroRNA Biogenesis and Regulation
- Pri-miRNA Transcription and Regulation
- Pri-miRNA Processing and Nuclear Export
- Maturation of miRNA RISC Formation
- Regulation of Mature miRNA by ceRNA
- Biological Roles of MicroRNA
- Gene Target Silencing
- Target Degradation Pathway
- Translational Repression
- miRNA-Mediated Gene Target Upregulation
- Enhanced Biological Impact of miRNAs Through Feedback Loops
- Positive Feedback Loop
- Negative Feedback Loop
- Switching Loops
- Biofluid-Based Biomarkers and Cell Communication
- Concluding Remarks and Future Directions
- Acknowledgments
- References
- Chapter 3-2: miRNAs and lncRNAs as Biomarkers of Toxicant Exposure
- Introduction
- miRNAs and Toxicological Response to Chemicals
- Endocrine Disruptor Chemicals and Altered miRNA Profile
- Bisphenol A
- Phthalates
- Exposure to Metals
- Exposure to Particles
- Nanoparticles
- Cigarette Smoking
- lncRNAs and Toxicological Response to Chemicals
- Endocrine Disruptor Chemicals and Altered lncRNA Profile
- Bisphenol A
- Exposure to Metals and lncRNA Expression
- Cigarette Smoking and lncRNA Profile
- Summary
- References
- Further Reading
- Section 4: Special Considerations in Toxicoepigenetics Research
- Chapter 4-1: Germline and Transgenerational Impacts of Toxicant Exposures
- Introduction
- The Germline
- Germline Specification and the Importance of the Epigenetic Repression of Somatic Fates
- PGC's Epigenetic Reprogramming: A Critical Period.